But now the real reason for the raid has been revealed in documents tendered to court and obtained by local media.

Sadly it has nothing to do with weaponised solar flares or aliens trying to make contact with us.

According to a search warrant, the observatory was shut down while FBI agents conducted computer forensic searches for child pornography, KTSM reported.

The document states the images were traced to an IP address used at the observatory and that a source within the building noticed pictures on a computer described as "not good", the warrant states.

The entrance to Sunspot Observatory is blocked off by yellow FBI tape in this photograph taken on September 14. Picture; Dylan Taylor-Lehman/Alamogordo Daily News via AP

An investigation by the FBI identified a janitor at the facility as the main suspect. However, he has not been charged with a crime even though his name appears on the warrant.

The warrant states the man would use the observatory Wi-Fi and a personal laptop to download the child pornography.

Agents were able to quickly narrow down their list of suspects thanks to the limited number of people with access to the facility between dusk and dawn.

The observatory, in the mountains of southern New Mexico, has a one-of-a-kind telescope that produces some of the sharpest images of the sun ever taken.

The FBI operation set alarm bells off across the internet as the curious and the paranoid discussed the possibilities.

Had astronomers found a lethal solar flare? Did the observatory receive a message from aliens? Could terrorists have worked out a way to weaponise the sun?

And was there a government cover up?

The Sunspot Solar Observatory in New Mexico has been the target of rampant speculation since the mysterious FBI raid. Picture: Supplied

After days of rampant speculation, the FBI referred all inquiries to The Association of Universities in Research for Astronomy (AURA), which is in charge of the observatory.

AURA fanned the flames of conspiracy by releasing a statement declaring a "security issue".

They offered scant detail but indicated that there had been a threat to people on the peak and that secrecy was necessary.

"We recognise that the lack of communications while the facility was vacated was concerning and frustrating for some," association spokeswoman Shari Lifson said.

"However, our desire to provide additional information had to be balanced against the risk that, if spread at the time, the news would alert the suspect and impede the law enforcement investigation. That was a risk we could not take."

The observatory reopened to the public on Monday and it seems that the raid has had a beneficial side effect - a boost in visitor numbers.

"Given the significant amount of publicity the temporary closure has generated, and the consequent expectation of an unusual number of visitors to the site, we are temporarily engaging a security service while the facility returns to a normal working environment," AURA said in a statement.

The Sunspot Solar Observatory was built in 1947 and sits atop Sacramento Peak above the tiny town of Sunspot in New Mexico.

It overlooks the Tularosa Basin - an expanse of desert that includes the city of Alamogordo, Holloman air force Base, White Sands Missile Range, White Sands National Monument and the site of the world's first atomic bomb test.

The telescope at Sunspot was originally built by the US air force. After several years of operation, it was transferred to the National Solar Observatory, which is part of the National Science Foundation.

Data from observations done at Sunspot is sent to New Mexico State University servers and can be used by researchers around the world.